In 1993, Cardinal Roger Mahony wrote to the Vatican with an urgent problem. One of his priests in the Archdiocese of Los Angeles had been accused of plying teenage boys with alcohol and molesting them, sometimes during prayer.

In less than eight years, Father Kevin Barmasse had, as one church official put it in newly released files, "left a wake of devastation that is hard to comprehend." Mahony yanked Barmasse out of his parish and wanted to make sure he couldn't return. But Barmasse appealed to the one body that could overrule Mahony: the Vatican.

"The case has been there for many, many months," Mahony wrote to one Vatican office tasked with handling priest misconduct. "The lengthy delay has created serious problems for my own credibility as a Diocesan Bishop."

In the wake of the court-ordered release of 12,000 pages of confidential archdiocese records, Mahony has been criticized for hiding abuse allegations from police and failing to protect parishioners from accused molesters. But the documents suggest that Mahony at times had to press an unresponsive Vatican to get molesting priests out of the church.

Although local leaders had the authority to take troubled clerics out of parishes, only the pope could remove them from the priesthood entirely. And when Mahony turned to the Vatican, the papers show, he ran into a bureaucracy steeped in ritual, mired in delays and reluctant to come to terms with the burgeoning problem.

"This was not just Mahony's experience. Anyone in the world who had dealings with the Vatican in the '80s and '90s was frustrated — who's in charge, what's the procedure, how long it took," said John Allen, a correspondent for the National Catholic Reporter who has written extensively on the Vatican.

Mahony dealt with multiple offices on abuse cases, including the Congregation for the Doctrine of the Faith, the Vatican office that defends church teaching and punishes those who commit delicta graviora — grave offenses. Joseph Ratzinger led the office for more than two decades before becoming Pope Benedict XVI in 2005. The pontiff recently announced that he will step down by month's end.

Mahony appeared to feel particularly impeded in dealing with Barmasse. The priest, who was accused of abusing at least eight teenage boys, had challenged Mahony's decision to remove him from ministry. As the appeal dragged on, Mahony told a Vatican official with the Congregation for the Clergy that he planned to visit Rome in December 1993. He suggested they meet in person — he would be staying, he wrote, at "Via della Conciliazione, 36 — very near to your offices." But even after his visit, the case remained unresolved.

Four months later, in March 1994, Mahony wrote: "Given the pastoral situation in the United States today, which is all too well known, Bishops need to be able to act quickly and decisively in cases of alleged clerical misconduct to assure the People of God that their rights are being fully protected."

In April, he wrote to the Vatican official: "It is now almost five months since my meeting with you and yet nothing further has come from you or your Congregation."

Another decade would pass before Barmasse was defrocked. Troy Gray, 44, who said Barmasse molested him in the late '80s while working in Tucson, cringed at the lengthy delay.

"They had their own procedures and protocols," he said in an interview. "It angers me that the children were put on the back burner."

Neither Mahony nor Vatican officials responded to requests for comment. In a 2010 interview with an Italian newspaper that the Vatican posted on its website, a top official at the Congregation for the Doctrine of the Faith said accusations that it moved glacially were "unjustified," particularly in recent years.

Observers said the Vatican response was markedly slower in decades past.

"This is not to give the American bishops a pass, but they really had no leadership from Rome," said Jason Berry, author of "Render Unto Rome: The Secret Life of Money in the Catholic Church."

Bishops started asking the Holy See in the 1980s for the power to remove abusers from the priesthood. But a formal request by American bishops was turned down by the Vatican in 1993, observers said.

At the Ratzinger-led Congregation for the Doctrine of the Faith, a staff of 45 was left "struggling to cope" with the caseload generated by the world's 400,000 priests, wrote Timothy Radcliffe, a Dominican priest who worked with the Vatican as head of the order from 1992 to 2001.

"It is generally imagined that the Vatican is a vast and efficient [organization]. In fact it is tiny," he wrote in a 2010 column for the British Catholic weekly The Tablet. "Documents slipped through the cracks. Cardinal Joseph Ratzinger lamented to me that the staff was simply too small for the job."

The labyrinthine protocol of the Vatican also made it ill-equipped to respond to a fast-evolving crisis. Each time bishops opened a case about a problematic priest, they cut a check to the Holy See for $500, a fee known as "taxa." Letters were sent to the Vatican embassy in Washington, D.C., then forwarded via diplomatic pouch. (Once, when Mahony seemed especially anxious for a response, he noted that he'd also sent the letter by fax.)

When one Los Angeles priest was defrocked in 2007, the files show, he was sent two notarized copies of the Latin decree, a third copy in English and instructions to write the date by his signature "with the month spelt out in full rather than using a number."

"It's not a court system," Berry said. "It's a system of tribunals in a monarchical form of government."

The Vatican began revamping how it handled sex abuse cases in 2001, when Ratzinger centralized them in the Congregation for the Doctrine of the Faith. The move has been hailed by observers as one of the Holy See's first concrete efforts to address the abuse crisis. Until Ratzinger became pope, he spent Friday mornings sifting through allegations of abuse from around the globe, work he reportedly called "our Friday penance."

Between 2001 and 2010, the office handled about 3,000 cases, the vast majority from the U.S., Msgr. Charles J. Scicluna, then the office's chief internal prosecutor, told the Italian paper. About 20% of the cases ended with the cleric being formally dismissed from the priesthood. In one such case, the documents show, Mahony asked the Holy See for a favor.

By 2004, when Father Carl Sutphin was 72 and living with his ailing mother, at least 16 people had accused him of molesting them decades before, sometimes while hearing their confessions. Sutphin said Mass for his mother every day, which Mahony called "one of her few remaining consolations in this world." The cardinal asked if Sutphin could remain a priest as long as she was alive.

The Vatican agreed. Although Sutphin was defrocked in December 2005, the Holy See held off notifying him until February 2006 — after officials learned that his mother had died.

Neither Sutphin nor Barmasse responded to requests for comment.

In another case, Mahony found himself in a familiar position: struggling with Vatican delays.

Father Arwyn Diesta's alleged sexual abuse of a seminary student first came to Mahony's attention in 1992. By then, the priest had returned to his native Philippines. Mahony wrote to Diesta's bishop, urging him to keep the priest away from teenage boys and have him undergo a psychological evaluation. When the bishop scoffed at the claims, Mahony went over his head.

"Obviously, if Father Diesta has indeed engaged in such sexual misconduct in the past, and I am convinced that he has, then he should not be in any ministry involving young people — especially young seminarians," Mahony told the Vatican office in charge of seminaries in 1993. The cardinal running the office, Pio Laghi, said he'd alert an archbishop in the Philippines.

In 2001, Mahony visited a U.S. military base in Okinawa — and ran into Diesta. He was working as a U.S. Navy chaplain and at a seminary in the Philippines.

Mahony again wrote to the Vatican, asking why nothing had been done. So did the mother of one alleged victim.

"How many other young men have been needlessly subjected to sexual abuse by Fr. Diesta since he was reported ... 10 years ago?" wrote the mother, who learned that Diesta was still in ministry through an Internet search.

In April 2002, the Vatican told Mahony that Diesta's bishop remained dead set against taking action. Nine years after Mahony's first letter, officials wrote: "We have forwarded the dossier on the aforementioned priest to the Congregation for the Doctrine of the Faith."

Clearly frustrated, Mahony tried to work around the Vatican. Over the next two years, the archdiocese reported the allegations against Diesta to church officials who worked with the military, the Los Angeles Police Department and child welfare officials in the Philippines.

Diesta could not be reached for comment. According to the Diocese of Sorsogon in the Philippines, he remains a parish priest.